Mark B. Gerstein Explained

Mark Gerstein
Birth Name:Mark Bender Gerstein
Birth Date:February 23
Citizenship:US
Fields:Bioinformatics
Thesis Title:Protein recognition: surfaces and conformational change
Thesis Url:http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282099
Thesis Year:1993
Academic Advisors:Michael Levitt (postdoc)
Doctoral Students:Werner Krebs[1] [2]

Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science., he is co-director of the Yale Computational Biology and Bioinformatics program.

Mark Gerstein is Albert L. Williams Professor of Biomedical Informatics, Professor of Molecular Biophysics & Biochemistry, Professor of Statistics & Data Science, and Professor of Computer Science at Yale University. In 2018, Gerstein was named co-director of the Yale Center for Biomedical Data Science.[3]

Education

After graduating from Harvard College summa cum laude with a Bachelor of Arts in physics in 1989,Gerstein did a PhD co-supervised by Ruth Lynden-Bell at the University of Cambridge and Cyrus Chothia at the Laboratory of Molecular Biology on conformational change in proteins, graduating in 1993.[4] He then went on to postdoctoral research in bioinformatics at Stanford University from 1993 to 1996 supervised by Nobel-laureate Michael Levitt.

Research

Gerstein does research in the field of bioinformatics.[5] [6] This involves applying a range of computational approaches to problems in molecular biology, including data mining and machine learning, molecular simulation, and database design. His research group has a number of foci including annotating the human genome,[7] personal genomics, cancer genomics, building tools in support of genome technologies (such as next-generation sequencing), analyzing molecular networks, and simulating macromolecular motions. Notable databases and tools that the group has developed include the Database of Macromolecular Motions,[1] [2] which categorizes macromolecular conformational change; tYNA,[8] which helps analyze molecular networks; PubNet,[9] which analyzes publication networks; PeakSeq,[10] which identifies regions in the genome bound by particular transcription factors; and CNVnator,[11] which categorizes block variants in the genome. Gerstein has also written extensively on how general issues in data science impact on genomics—in particular, in relation to privacy[12] and to structuring scientific communication.[13]

Gerstein's work has been published in peer reviewed scientific journals[14] and non-scientific publications in more popular forums.[15] His work has been highly cited, with an H greater than 100. He serves on a number of editorial and advisory boards, including those of PLoS Computational Biology, Genome Research, Genome Biology, and Molecular Systems Biology. He has been quoted in the New York Times,[16] [17] [18] including on the front page,[7] and in other major newspapers.[19]

Awards and honors

In addition to a W. M. Keck Foundation Distinguished Young Scholars award,[20] Gerstein has received awards from the US Navy, IBM, Pharmaceutical Research and Manufacturers of America, and the Donaghue Foundation.[21] He is a Fellow of the AAAS. Other awards include a Herchel-Smith Scholarship supporting his doctoral work at Emmanuel College, Cambridge and a Damon Runyon Cancer Research Foundation Postdoctoral Fellowship. He is a contributor to a number of scientific consortia including ENCODE,[22] modENCODE,[23] [24] [25] 1000 Genomes Project, Brainspan,[26] and DOE Kbase. He was made a Fellow of the International Society for Computational Biology in 2015.[27]

External links

Notes and References

  1. PhD . Werner G.. Krebs . The database of macromolecular motions : a standardized system for analyzing and visualizing macromolecular motions in a database framework . Yale University . 2002. 54626123.
  2. 9722650. 147832. 1998. Gerstein. M. A database of macromolecular motions. Nucleic Acids Research. 26. 18. 4280–90. Krebs. W . 10.1093/nar/26.18.4280.
  3. Web site: Amy . Xiong . February 9, 2018. Yale establishes biomedical data science center. 2020-09-27. yaledailynews.com. en.
  4. PhD . Mark. Gerstein . Protein recognition: surfaces and conformational change . University of Cambridge . 1993 . Mark Bender Gerstein.
  5. Durbin . R. M. . Richard M. Durbin. Abecasis . G. R.. Gonçalo Abecasis . Altshuler . R. M. . Auton . G. A. R. . Brooks . D. R. . Durbin . A. . Gibbs . A. G. . Hurles . F. S. . McVean . F. M. . Donnelly . 10.1038/nature09534 . P. . Egholm . M. . Flicek . P. . Gabriel . S. B. . Gibbs . R. A. . Knoppers . B. M. . Lander . E. S. . Lehrach . H. . Mardis . E. R. . McVean . G. A. . Nickerson . D. A. . Peltonen . L. . Schafer . A. J. . Sherry . S. T. . Wang . J. . Wilson . R. K. . Gibbs . R. A. . Deiros . D. . Metzker . M. . Muzny . D. . Reid . J. . A map of human genome variation from population-scale sequencing . Nature . 467 . 7319 . 1061–1073 . 2010 . 20981092. 3042601 . 2010Natur.467.1061T. 29 .
  6. Wang . Z. . Gerstein . M. . Snyder . M. . 10.1038/nrg2484 . RNA-Seq: A revolutionary tool for transcriptomics . Nature Reviews Genetics . 10 . 1 . 57–63 . 2009 . 19015660 . 2949280 .
  7. Gina Kolata, (Sept. 5, 2012) 'Bits of Mystery DNA, Far From Junk, Play Crucial Role,' NY Times
  8. 17021160. 2006. Yip. K. Y.. The tYNA platform for comparative interactomics: A web tool for managing, comparing and mining multiple networks. Bioinformatics. 22. 23. 2968–70. Yu. H. Kim. P. M.. Schultz. M. Gerstein. M. 10.1093/bioinformatics/btl488. free.
  9. Douglas . S. M. . Montelione . G. T. . Gerstein . M. . PubNet: A flexible system for visualizing literature derived networks . Genome Biology . 6 . 9 . R80 . 10.1186/gb-2005-6-9-r80 . 2005 . 1242215 . 16168087. free .
  10. 19122651. 2924752. 2009. Rozowsky. J. Peak Seq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology. 27. 1. 66–75. Euskirchen. G. Auerbach. R. K.. Zhang. Z. D.. Gibson. T. Bjornson. R. Carriero. N. Snyder. M. Gerstein. M. B.. 10.1038/nbt.1518.
  11. 21324876. 3106330. 2011. Abyzov. A. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research. 21. 6. 974–84. Urban. A. E.. Snyder. M. Gerstein. M. 10.1101/gr.114876.110.
  12. 22144881. 3228779. 2011. Greenbaum. D. Genomics and privacy: Implications of the new reality of closed data for the field. PLOS Computational Biology. 7. 12. e1002278. Sboner. A. Mu. X. J.. Gerstein. M. 10.1371/journal.pcbi.1002278. 2011PLSCB...7E2278G. free.
  13. 17495904. 2007. Gerstein. M. Structured digital abstract makes text mining easy. Nature. 447. 7141. 142. Seringhaus. M. Fields. S. 10.1038/447142a. 2007Natur.447..142G. free.
  14. Giaever . G. . Chu . A. M. . Ni . L. . Connelly . C. . Riles . L. . Véronneau . S. . Dow . S. . Lucau-Danila . A. . Anderson . K. . André . 10.1038/nature00935 . B. . Arkin . A. P. . Astromoff . A. . El-Bakkoury . M. . Bangham . R. . Benito . R. . Brachat . S. . Campanaro . S. . Curtiss . M. . Davis . K. . Deutschbauer . A. . Entian . K. D. . Flaherty . P. . Foury . F. . Garfinkel . D. J. . Gerstein . M. . Gotte . D. . Güldener . U. . Hegemann . J. H. . Hempel . S. . Herman . Z. . Functional profiling of the Saccharomyces cerevisiae genome . Nature . 418 . 6896 . 387–391 . 2002 . 12140549 . 2002Natur.418..387G. 4400400 .
  15. Web site: List of Non-technical Writing by Mark Gerstein. https://web.archive.org/web/20131017061104/http://info.gersteinlab.org/Other_Papers. 2013-10-17. gersteinlab.org.
  16. News: Poking Holes in Genetic Privacy. The New York Times. 2013-06-16. 2016-01-18. 0362-4331. Gina. Kolata.
  17. News: Tiny, Vast Windows Into Human DNA. The New York Times. 2014-09-01. 2016-01-18. 0362-4331. Carl. Zimmer.
  18. News: Thoughts on Genes. The New York Times. 2008-11-10. 2016-01-18. 0362-4331.
  19. Web site: Scientists Unveil New Blueprint Of How The Human Genome Works. courant.com. 2016-01-18.
  20. Mervis. Jeffrey. 1999-07-16. Keck Helps Five Careers With $1 Million Grants. Science. English. 285. 5426. 312–3. 10.1126/science.285.5426.312b. 10438290. 33084600.
  21. Web site: Donaghue Foundation selects five investigators for long-term support. 2020-09-27. medicine.yale.edu. en.
  22. Ewan Birney . John Stamatoyannopoulos . Anindya Dutta . ENCODE Project Consortium. Birney E. Stamatoyannopoulos JA. Dutta A . Guigó R. Gingeras TR. Margulies EH. Weng Z. Snyder M. Dermitzakis ET. 10.1038/nature05874 . Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project . Nature . 447 . 7146 . 799–816 . 2007 . 17571346 . 2212820 . 2007Natur.447..799B . etal.
  23. Landt . S. G. . Marinov . G. K. . Kundaje . A. . Kheradpour . P. . Pauli . F. . Batzoglou . S. . Bernstein . B. E. . Bickel . P. . Brown . J. B. . Cayting . P. . Chen . Y. . Desalvo . G. . Epstein . C. . Fisher-Aylor . K. I. . Euskirchen . G. . Gerstein . M. . Gertz . J. . Hartemink . A. J. . Hoffman . M. M. . Iyer . V. R. . Jung . Y. L. . Karmakar . S. . Kellis . M. . Kharchenko . P. V. . Li . Q. . Liu . T. . Liu . X. S. . Ma . L. . Milosavljevic . A. . Myers . R. M. . ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia . Genome Research . 22 . 9 . 1813–1831 . 2012 . 10.1101/gr.136184.111 . 22955991 . 3431496 .
  24. Cheng . C. . Yan . K. K. . Yip . K. Y. . Rozowsky . J. . Alexander . R. . Shou . C. . Gerstein . M. . Mark Bender Gerstein. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets . Genome Biology . 12 . 2 . R15 . 2011 . 10.1186/gb-2011-12-2-r15 . 21324173 . 3188797 . free .
  25. Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A . 10.1126/science.1196914 . Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project . Science . 330 . 6012 . 1775–1787 . 2010 . 21177976. 3142569. 2010Sci...330.1775G . etal.
  26. Li. Mingfeng. Santpere. Gabriel. Kawasawa. Yuka Imamura. Evgrafov. Oleg V.. Gulden. Forrest O.. Pochareddy. Sirisha. Sunkin. Susan M.. Li. Zhen. Shin. Yurae. Zhu. Ying. Sousa. André M. M.. 2018-12-14. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science. 362. 6420. eaat7615. 10.1126/science.aat7615. 0036-8075. 6413317. 30545854. 2018Sci...362.7615L.
  27. Web site: Meet the ISCB Fellows Class of 2015. https://web.archive.org/web/20150220233807/http://www.iscb.org/iscb-news-items/2392-2015feb20-meet-the-iscb-fellows-class-of-2015. 2015-02-20. International Society for Computational Biology.

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